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Could you provide an example? |
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Yes of course, you'll find in copy a file containing all the data with which I made the "set.000" thanks to the "raw to set" script. |
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Dear Developers,
I am trying to calculate the sel of a system using the dp neighbor-stat tool, but it is returning an empty sel except for one of the atom types (H).
I have a periodic system in a hexagonal unit cell. This system contains 4 atom types: "Br H Mo O," labeled respectively "0 1 2 3" in the type.raw and type_map.raw files.
I am using deepMD-kit V2.2.10, and the command line is:
dp neighbor-stat -s init_MoBr -r 6.0 -t Br H Mo O
The output is the following:
DEEPMD INFO training data with min nbor dist: 0.4716052460030911
DEEPMD INFO training data with max nbor size: [ 0 189 0 0]
DEEPMD INFO min_nbor_dist: 0.471605
DEEPMD INFO max_nbor_size: [ 0 189 0 0]
I’ve never had this problem before. I’ve verified that all the units for the coordinates and the box.raw are in Ångström.
I also tried increasing the cutoff, but this only resulted in increasing the number of H neighbors in the cell.
I tried using a cubic sel since it’s the first time I’m training on a hexagonal system, but there were no changes.
Maybe I am incorrectly converting the cell parameters to Cartesian coordinates:
ABC [angstrom] 15.297 15.297 11.219
ALPHA_BETA_GAMMA [deg] 90.0 90.0 120.0
Gives : (xx xy xz yx yy yz zx zy zz)
15.297 -7.6485 0 0 13.2454 0 0 0 11.219
But even if something is wrong, I think that I should still have other atoms detected.
Any help is would be much appreciated!
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